Islamic Action Front (IAF) candidates were confirmed winners in just six of the 22 seats they contested, down from 17 in the last parliament.
It said its own polling indicated at least 16 IAF members should have won.
The interior minister denied any fraud, saying the government had conducted "impartial and fair" elections.
IAF spokesman Jamil Abu Bakr called for a rerun of polling in constituencies where he said fraud had occurred.
"This is an electoral massacre... violations by far exceeded even the last elections... it will have harmful repercussions on the country's political progress," he said.
He pointed to the results in Zarqa, a traditional Islamist stronghold, where the IAF failed to win a single seat.
Tribal areas
Results were announced by Interior Minister Eid al-Fayez at a news conference in
Officials admitted that 17 people had been arrested on suspicion of interfering with the electoral process, including two for alleged vote-buying.
But Mr Eid said accusations of widespread vote-rigging "had been exaggerated by the media".
The IAF fielded candidates in a fifth of the 110 seats, but only after receiving assurances from the government that the vote would be fair.
"Our mistake was that we believed in government promises," an unnamed Islamist politician told AFP.
Critics of the electoral system say it is tailored to counter popular support of Islamist and liberal opposition candidates in urban areas.
Staunchly conservative tribal areas are over-represented in parliament, with each MP representing 2,000-3,000 voters, compared with more than 90,000 voters per MP in the capital
Correspondents say a number of Islamist sympathizers ran as independents but none of them succeeded in winning a seat.
Real power rests with the king in Jordan, who appoints governments, approves legislation and is able to dissolve parliament.
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Jordanian voter